Write a vcf file from a tidy data frame

Write a vcf file (file format version 4.3, see details below) from a tidy data frame. Used internally in genometranslator and might be of interest for users. This writer translates the supplied calls; it does not apply VCF quality filters. Resolve marker, sample, genotype-quality, and missingness filtering before export according to the downstream use of the VCF.

Usage

write_vcf(data, strata = FALSE, filename = NULL, source = NULL, empty = FALSE)

Arguments

data

A tidy data frame object in the global environment or a tidy data frame in wide or long format in the working directory. How to get a tidy data frame ? Look into genometranslator tidy_genome.

strata

(optional, logical) Should the strata information be included in the FORMAT field (along the GT info for each samples ?). To make the VCF population-ready use strata = TRUE. The strata information must be included in the STRATA column of the tidy dataset. Default: strata = FALSE. Experimental.

filename

(optional) The file name prefix for the vcf file written to the working directory. With default: filename = NULL, the date and time is appended to radiator_vcf_file_. Default: filename = NULL.

source

source of vcf Default: source = NULL.

empty

generate an empty vcf. Default: empty = FALSE.

Details

VCF file format version:

If you need a different file format version than the current one, just change the version inside the newly created VCF, that should do the trick. For more information on Variant Call Format specifications.

Data filtering

This writer does not silently filter markers or individuals. It may validate requirements imposed by the destination format and stop with an informative error when the input is unsuitable. It is the user's responsibility to filter and quality-control the data appropriately for the intended analysis before generating the output. Use radr or another suitable workflow when filtering is required.

Dependencies

Required package dependencies are declared in DESCRIPTION and are installed with genometranslator. Any additional dependency needed only for this format or option is identified in this help page. Use genometranslator_dependencies() to inspect the availability of core packages, optional packages, and external executables.

References

Danecek P, Auton A, Abecasis G et al. (2011) The variant call format and VCFtools. Bioinformatics, 27, 2156-2158.

Author

Thierry Gosselin thierrygosselin@icloud.com